[2018-10-12 23:06:47] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:06:47] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:06:47] Checking for Bowtie index files (genome)..
[2018-10-12 23:06:47] Checking for reference FASTA file
[2018-10-12 23:06:47] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:06:51] Reading known junctions from GTF file
[2018-10-12 23:06:55] Preparing reads
	 left reads: min. length=100, max. length=100, 265735 kept reads (207 discarded)
	right reads: min. length=100, max. length=100, 265538 kept reads (404 discarded)
[2018-10-12 23:07:08] Building transcriptome data files /scratch/8792825.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:07:29] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:15:56] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:16:23] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:16:51] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:16:51] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:17:23] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:17:32] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:17:43] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:17:51] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:18:00] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:18:33] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:18:41] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:18:52] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:19:01] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:19:10] Searching for junctions via segment mapping
[2018-10-12 23:21:44] Retrieving sequences for splices
[2018-10-12 23:23:54] Indexing splices
[2018-10-12 23:24:14] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:24:18] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:24:23] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:24:27] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:24:32] Joining segment hits
[2018-10-12 23:26:47] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:26:51] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:26:56] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:27:01] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:27:05] Joining segment hits
[2018-10-12 23:29:32] Reporting output tracks
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[2018-10-12 23:32:44] A summary of the alignment counts can be found in /scratch/8792825.1.linga/tophat2/align_summary.txt
[2018-10-12 23:32:44] Run complete: 00:25:57 elapsed